of whole genome sequences of many different pathogenic and commensal
forms of microorganisms have improved our perception of the mechanisms
of pathogenesis and the transition between pathogenic and
non-pathogenic varieties within the same species. It is becoming
increasingly evident that distinct genomic differences found in
different microbes have a definite impact on pathogenic potential,
adaptation to parasitic lifestyles and host/tissue tropism. Some
examples in this context are discussed.
In the case where
different species of the same genus represent diverse lifestyles it is
imperative to have sampled genome sequences from varieties of all
forms. For example, the availability of three complete genome sequences
from Acinetobacter (i.e. AYE, SDF and A. baylyi ADP1) has enabled comparison in a more general context to tease apart likely genetic changes that enabled adaptation of Acinetobacter species to specific environments .
While the three organisms share a large chunk of genes, major
differences exist in terms of their flexible genome component such as
prophages and insertional sequences .
Another interesting lifestyle has been deciphered from the genome sequence of Brachyspira hyodysenteriae ,
an anaerobic intestinal spirochaete that colonizes niches of swine
colon and causes dysentery of pigs, a disease of significant economic
importance. It appears that the bacterium may have evolved strategies
to survive and adapt via gene transfer in the intestinal environment.
The genome sequence data suggests presence of genes encoding anaerobic
metabolism and mechanisms to cause mucosal damage through the activity
of many different virulence factors facilitated by chemotaxis and
motility. Interestingly, the chunks of genes believed to have been
horizontally acquired by Brachyspira, and that are supposed to
have facilitated adaptation and survival of the bacterium within the
intestines, belonged mostly to classically ‘enteric type’ of organisms,
rather than to other spirochaetal relatives of Brachyspira .
Whole genome sequencing and analysis of Mycobacterium indicus pranii (MIP) together with molecular phylogenetic analyses  revealed a unique soil and water dwelling lifestyle for this ‘generalist’ organism. MIP had a common ancestor with pathogenic Mycobacterium avium intracellulare
complex that did not prefer parasitic adaptation but a free living
life-style. Further analysis suggests a shared aquatic phase of MIP
with the early pathogenic forms of Mycobacterium, well before
the latter diverged to form ‘specialist’ bacterial parasites. This
information has an important bearing on our understanding of
and streamlining has been a dominant evolutionary trend in
mycobacterial genome evolution that perhaps shapes their host-range and
tissue tropism giving rise to ‘specialist’ lineages , . Another interesting example of genome optimization through reduction - based - metabolic optimization comes from Yersinia pestis which originated from its closest relative Y. pseudotuberculosis . The same has been true in the case of Brucella ovis whose genome is shorter than the classical zoonotic strains  oving to loss of genes via pseudogenization and degradation that has happened concomitant to the narrowing of its host range; it infects only sheep .
It has been suggested that inactivation of genes linked to nutrient
acquisition and utilization, cell envelope structure and those encoding
urease may have played a role in narrowing of the tissue predilection
and host range of B. ovis . Another important feature of the B. ovis
genome has been the presence of increased number of transposable
elements thus hinting towards frequent shuffling (genomic fluidity, or
plasticity) of its genome .
Variation in gene
content, especially the flexible or unstable part of the genome such as
mobile elements and genomic islands, has been shown to influence
phenotypes such as virulence and antimicrobial resistance. This is
especially true for some of the biomedically significant organisms such
as the Group A Streptococcus (GAS). Recently, a study analyzing twelve sequenced GAS genomes 
determined that the resultant ‘metagenome’ holds tremendous potential
for understanding pathobiology of the GAS. This multi-genome dataset
provides an opportunity to address putative functions, encoded by the
exogenous genetic elements, such as antimicrobial resistance. Another
major benefit from these genomes includes the ability to develop
molecular markers based on GAS mobile elements to tag and track
field-level diversity of the circulating strains; this will be of
paramount significance in vaccine development and testing.